Short across pins 5 & 8

I'm working on an robot with my Arduino Mega ADK board. I had some h-bridges lying around so I made my own motor shield. After working for awhile, it all of sudden quit. I was troubleshooting with my multimeter in continuity mode. I discovered that, when the board is on, even with nothing else attached, pins 5 & 8 - which were attached to the same h-bridge - were shorted together. With the board off, they aren't. I tried a few other pin combinations, and they don't beep the tester.

Is something wrong with my board? If so is there a fix? If not, any reason I can't just avoid those pins?
Any idea what may have caused this?

I did connect to a cheapie power supply set to 9V, despite having seen this: YIHUA PS-3010D LAB POWER SUPPLY REVIEW AND REPAIR - YouTube

I'd suspect that continuity measurements in a live circuit are not trustworthy.

I'd go further and say that continuity measurements in a live circuit, unless measuring something simple like relay contacts not otherwise connected, are meaningless.

You need to test that the Arduino pins still work disconnected, then check that
when connected to the H-bridge they still respond (if not the H-bridge may be fried).

If you suspect the Hbridge is damaged use 5V for both logic and motor supplies and
don't attach the motor during testing the Arduino pins.

Read the "Remember" section:

http://www.ladyada.net/library/metertut/continuity.html

MarkT:
You need to test that the Arduino pins still work disconnected, then check that
when connected to the H-bridge they still respond (if not the H-bridge may be fried).

If you suspect the Hbridge is damaged use 5V for both logic and motor supplies and
don't attach the motor during testing the Arduino pins.

I wrote a sketch that toggled the pins between high and low every 3 seconds. I put a resistor (220 ohm) between each pin and ground and attached the multimeter in parallel with the resistor. Each pin toggled between about 4.5V and 0V. That's a good test, right?

Next I'm gonna test the Hbridges. I have 4 SN754410NE's. One is short between one of the motor out pins and ground pins, so I'm pretty sure it's shot. I can't get the motor to work (on the shield or on the breadboard) with any of the other 3. If they are shot, what might be the culprit? Each H-bridge is set up to control a pair of small motors wired in parallel (for equal voltage i think?) - i.e. two of the motors on this:

That h-bridge is supposed to be able to handle 1.1 A.
Those motors aren't real powerful:
No-load current(3V):60mA
No-load current(6V):71mA
Stall current(3V):260mA
Stall current(6V):470mA

I set up the multimeter to measure the amp draw from the 2 motors on a side running at 9 volts. (in series, before the motors split into the 2 parallels). Running it pulls 350 mA. Stalled out (me holding the wheels) it pulls 900 mA. This shouldn't fry h-bridges that easily?

fatweasel:
I wrote a sketch that toggled the pins between high and low every 3 seconds. I put a resistor (220 ohm) between each pin and ground and attached the multimeter in parallel with the resistor. Each pin toggled between about 4.5V and 0V. That's a good test, right?

Yes, it's good. According to the spec sheet, 4.5V is what you get when you are sourcing 20mA current at room temperature with an output pin. I don't know enough about H-bridge for the rest of your questions though.

The SN754410 has integral flyback diodes so its a bit of a mystery how it got damaged -
perhaps an accidental short circuit on one of its outputs? Poor ground connection?